# Source code for openquake.commonlib.util

```
# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# Copyright (C) 2015-2020 GEM Foundation
#
# OpenQuake is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# OpenQuake is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with OpenQuake. If not, see <http://www.gnu.org/licenses/>.
import numpy
from openquake.baselib import config, datastore
from openquake.commonlib import logs
F32 = numpy.float32
[docs]def read(calc_id, username=None):
"""
:param calc_id: a calculation ID
:param username: if given, restrict the search to the user's calculations
:returns: the associated DataStore instance
"""
if isinstance(calc_id, str) or calc_id < 0 and not username:
# get the last calculation in the datastore of the current user
return datastore.read(calc_id)
job = logs.dbcmd('get_job', calc_id, username)
if job:
return datastore.read(job.ds_calc_dir + '.hdf5')
else:
# calc_id can be present in the datastore and not in the database:
# this happens if the calculation was run with `oq run`
return datastore.read(calc_id)
[docs]def max_rel_diff(curve_ref, curve, min_value=0.01):
"""
Compute the maximum relative difference between two curves. Only values
greather or equal than the min_value are considered.
>>> curve_ref = [0.01, 0.02, 0.03, 0.05, 1.0]
>>> curve = [0.011, 0.021, 0.031, 0.051, 1.0]
>>> round(max_rel_diff(curve_ref, curve), 2)
0.1
"""
assert len(curve_ref) == len(curve), (len(curve_ref), len(curve))
assert len(curve), 'The curves are empty!'
max_diff = 0
for c1, c2 in zip(curve_ref, curve):
if c1 >= min_value:
max_diff = max(max_diff, abs(c1 - c2) / c1)
return max_diff
[docs]def max_rel_diff_index(curve_ref, curve, min_value=0.01):
"""
Compute the maximum relative difference between two sets of curves.
Only values greather or equal than the min_value are considered.
Return both the maximum difference and its location (array index).
>>> curve_refs = [[0.01, 0.02, 0.03, 0.05], [0.01, 0.02, 0.04, 0.06]]
>>> curves = [[0.011, 0.021, 0.031, 0.051], [0.012, 0.022, 0.032, 0.051]]
>>> max_rel_diff_index(curve_refs, curves)
(0.2, 1)
"""
assert len(curve_ref) == len(curve), (len(curve_ref), len(curve))
assert len(curve), 'The curves are empty!'
diffs = [max_rel_diff(c1, c2, min_value)
for c1, c2 in zip(curve_ref, curve)]
maxdiff = max(diffs)
maxindex = diffs.index(maxdiff)
return maxdiff, maxindex
[docs]def rmsep(array_ref, array, min_value=0):
"""
Root Mean Square Error Percentage for two arrays.
:param array_ref: reference array
:param array: another array
:param min_value: compare only the elements larger than min_value
:returns: the relative distance between the arrays
>>> curve_ref = numpy.array([[0.01, 0.02, 0.03, 0.05],
... [0.01, 0.02, 0.04, 0.06]])
>>> curve = numpy.array([[0.011, 0.021, 0.031, 0.051],
... [0.012, 0.022, 0.032, 0.051]])
>>> str(round(rmsep(curve_ref, curve, .01), 5))
'0.11292'
"""
bigvalues = array_ref > min_value
reldiffsquare = (1. - array[bigvalues] / array_ref[bigvalues]) ** 2
return numpy.sqrt(reldiffsquare.mean())
[docs]def log(array, cutoff):
"""
Compute the logarithm of an array with a cutoff on the small values
"""
arr = numpy.copy(array)
arr[arr < cutoff] = cutoff
return numpy.log(arr)
[docs]def closest_to_ref(arrays, ref, cutoff=1E-12):
"""
:param arrays: a sequence of arrays
:param ref: the reference array
:returns: a list of indices ordered by closeness
This function is used to extract the realization closest to the mean in
disaggregation. For instance, if there are 2 realizations with indices
0 and 1, the first hazard curve having values
>>> c0 = numpy.array([.99, .97, .5, .1])
and the second hazard curve having values
>>> c1 = numpy.array([.98, .96, .45, .09])
with weights 0.6 and 0.4 and mean
>>> mean = numpy.average([c0, c1], axis=0, weights=[0.6, 0.4])
then calling ``closest_to_ref`` will returns the indices 0 and 1
respectively:
>>> closest_to_ref([c0, c1], mean)
[0, 1]
This means that the realization 0 is the closest to the mean, as expected,
since it has a larger weight. You can check that it is indeed true by
computing the sum of the quadratic deviations:
>>> ((c0 - mean)**2).sum()
0.0004480000000000008
>>> ((c1 - mean)**2).sum()
0.0010079999999999985
If the 2 realizations have equal weights the distance from the mean will be
the same. In that case both the realizations will be okay; the one that
will be chosen by ``closest_to_ref`` depends on the magic of floating point
approximation (theoretically identical distances will likely be different
as numpy.float64 numbers) or on the magic of Python ``list.sort``.
"""
dist = numpy.zeros(len(arrays))
logref = log(ref, cutoff)
pairs = []
for idx, array in enumerate(arrays):
diff = log(array, cutoff) - logref
dist = numpy.sqrt((diff * diff).sum())
pairs.append((dist, idx))
pairs.sort()
return [idx for dist, idx in pairs]
[docs]def compose_arrays(a1, a2, firstfield='etag'):
"""
Compose composite arrays by generating an extended datatype containing
all the fields. The two arrays must have the same length.
"""
assert len(a1) == len(a2), (len(a1), len(a2))
if a1.dtype.names is None and len(a1.shape) == 1:
# the first array is not composite, but it is one-dimensional
a1 = numpy.array(a1, numpy.dtype([(firstfield, a1.dtype)]))
fields1 = [(f, a1.dtype.fields[f][0]) for f in a1.dtype.names]
if a2.dtype.names is None: # the second array is not composite
assert len(a2.shape) == 2, a2.shape
width = a2.shape[1]
fields2 = [('value%d' % i, a2.dtype) for i in range(width)]
composite = numpy.zeros(a1.shape, numpy.dtype(fields1 + fields2))
for f1 in dict(fields1):
composite[f1] = a1[f1]
for i in range(width):
composite['value%d' % i] = a2[:, i]
return composite
fields2 = [(f, a2.dtype.fields[f][0]) for f in a2.dtype.names]
composite = numpy.zeros(a1.shape, numpy.dtype(fields1 + fields2))
for f1 in dict(fields1):
composite[f1] = a1[f1]
for f2 in dict(fields2):
composite[f2] = a2[f2]
return composite
[docs]def get_assets(dstore):
"""
:param dstore: a datastore with keys 'assetcol'
:returns: an array of records (id, tag1, ..., tagN, lon, lat)
"""
assetcol = dstore['assetcol']
tagnames = sorted(assetcol.tagnames)
tag = {t: getattr(assetcol.tagcol, t) for t in tagnames}
dtlist = [('id', '<S100')]
for tagname in tagnames:
dtlist.append((tagname, '<S100'))
dtlist.extend([('lon', F32), ('lat', F32)])
asset_data = []
for a in assetcol.array:
tup = tuple(b'%s' % tag[t][a[t]].encode('utf-8') for t in tagnames)
asset_data.append((a['id'],) + tup + (a['lon'], a['lat']))
return numpy.array(asset_data, dtlist)
```